The Red Report Transgression
by WeBuiltThePyramids
Summary: When a man who has murdered two people goes after Penny, the gang meets the CBI team assigned to their case. What does the man want? Was Penny the intended target? Does it have to do with Leonard? The CBI team heads to Nerdvana.
1. Chapter 1

**For those of you who do not watch both of these shows: The Big Bang Theory titles always begin with "the" and are written like a scientific principle. The Mentalist always has "red" or a word meaning "red" in the title. So I combined the two traditions in my title.**

**Shows Involved: The Big Bang Theory, CBS, and The Mentalist, CBS**

**Pairings: Leonard and Penny: The Big Bang Theory. Howard and Bernadette: The Big Bang Theory. The Mentalist: Flirtation between Patrick Jane and Teresa Lisbon that can be interpreted as platonic or romantic, whichever the individual prefers.**

**This fic will have no deaths of any main character in either show.**

**This will probably be easier to understand if you watch The Big Bang Theory. It may be harder to get if you only watch The Mentalist, but I'll try to explain stuff within the story if I can. If you don't get something (from either show), PM me and I will catch you up.**

**DISCLAIMER: I own absolutely NADA!**

"I really hate little cars," Leonard said, leaning forward and gripping the steering wheel tightly.

"I don't see what the big deal is," Sheldon said from the passenger seat. "Considering the size of yourself. This is the perfect homunculus car, and it gets excellent gas mileage."

"Sheldon, shut up. I'm trying to focus." Leonard's brow was sweaty, but he didn't dare take a hand of the wheel to wipe his brow. The highway was packed with quick-moving semi-trucks, and in the event of a crash his little car wouldn't stand a chance. It was night time, and Leonard had a horrible fear that, even with his lights, they wouldn't be able to see him even if there was no accident.

Sheldon cocked his head and looked at his best friend hunched over the wheel. "What are you doing?"

"Trying to get us home safe."

There was a pause. "Trying to get us…"

"Okay fine, Sheldon. Home _safely_, are you happy now? Now be quiet so I can do that. Remember it's not my fault you decided to run off to Texas again."

"As I explained to you, I did not _run off _to Texas." Sheldon opened his mouth to speak again, then closed it. "Leonard, your phone is ringing."

"Yeah, I hear it," he said through gritted teeth.

Sheldon was silent for a moment. "Aren't you going to answer it?"

"I'm driving, Sheldon. If it's important, they'll leave a voicemail."

"You don't check your voicemail."

"I will when we get home, okay?"

Sheldon's face twitched. "Answer the phone, Leonard!"

"Don't start this again!"

Leonard sighed. It was late and he was irritable and tired and sick of driving.

When they got home, Leonard dumped Sheldon's stuff on the floor in the living room and went straight to bed. Penny wasn't sleeping at his place, but she hadn't expected him to be back that night. He didn't bother going next door-he'd see her in the morning and right now he didn't want to talk or fornicate, just sleep. He slung off his jacket and jeans and fell into his bed. His eyes were so tired that it was easy to fall asleep.

* * *

The next morning he awoke way too early and with an awful headache-and only to be pestered by Sheldon to drive him to the comic book store. "The comic book store is not open yet, Sheldon."

"Yes it is, Leonard. I just got a text from Stuart. 'The new Flash is in-it will blow your mind.' Now that my mind is pre-blown, I need to get there as soon as possible to find out what made it blown."

"Dammit, fine." Leonard begrudgingly, pulling on his I-don't-give-a-rat's-behind clothes and grabbing the keys. He was not happy about this. More driving.

He left Sheldon there and went home, eager to relax. He was sitting in the living room drinking coffee when there was a knock at the door. Getting up, he opened it. Standing outside were two women he'd never seen before, one with dark hair and the other a redhead, dressed in professional clothing. The dark-haired woman held up a badge. "Agent Lisbon, California Bureau of Investigation. This is Agent Van Pelt. Are you Leonard Hofstadter?"

Leonard frowned. "Um…yes. Yes, I am."

"We'd like to ask you a few questions about your neighbor, Penny. May we come in?"

Leonard blinked. "Penny? Where is she? What happened?" He stood aside and let the women in. "What's going on?"

"You don't know?" Asked Van Pelt, sitting next to Lisbon on the couch.

Leonard was more than a little concerned now. He sank into the white chair. "No…I don't know anything. What happened? Is she okay?"

"She was…-"

"Hold on." Lisbon silenced Van Pelt. "Where's Jane?"

"Sorry, here I am." A tall man with curly blonde hair entered the room. "I was checking out the elevator. Terrible. Horrible. It must be fixed."

"Sit down," Lisbon said sternly.

"Sorry." He sat on the couch next to Lisbon. "Patrick Jane, consultant."

"Yeah, yeah, nice to meet you. What's wrong with Penny?"

"She was found this morning on the side of the road about twenty minutes from here, badly beaten. Unconcious." Jane said matter-of-factly. "Just horrible. She's at the hospital now. Where were you last night?"

"You think I did this?" Leonard was numb, incredulous. Last night, while he'd been sleeping, Penny'd been _beaten_? "I didn't do this!" He stood up. "How _dare_ you accuse me!"

"What is the matter with you?" Lisbon asked Jane angrily.

"Oh, I was just testing him." He looked up at Leonard and smiled. "You did very well." Looking back at Lisbon he said, "He didn't do it."

"We don't know that. Do you have an alibi for last night?" Lisbon asked Leonard.

"We do know that, actually," Jane said. "Did you see his face? His eyes? He's genuinely concerned for her. He cares about her, and he'd never harm her, not for money or for revenge. I'd say he's not the type to harm anyone, but she has a special importance to him."

Lisbon glared at Jane. "If he has an alibi, then that will give us something solid for him. Do you have one?" She looked back at Leonard.

"Yes." He nodded. "I was driving my roommate, Sheldon Cooper, home from Texas. We got home late."

"You two involved?"

"Penny and I? Yes, we are."

"What about you and Mr. Cooper?"

"What? No!" Leonard tried to explain. "We work at the university. We live together, but in heterosexual bedrooms. Actually, Sheldon has no 'deal'. Not girls, not guys, not sock puppets…" He trailed off. "He can vouch for me. His mother can vouch for me…heck, any of about thirty scary men in semi-trucks can vouch for me. How bad _is_ Penny? Is she awake?"

"She's bruised up, black eye, but that's about it. She's in good spirits."

"Can I see her?"

"If you come with us, we can arrange that for you."

"Thank you." He bit his lip. "Can I change?" He was still wearing his I-don't-give-a-rat's-behind clothes and his hair was sticking up in all directions.

"We can wait," said Van Pelt, smiling as she and the other two stood. "We'll just be outside."

"Okay," he said. "One question, real quick. Don't you guys do homicide investigations?"

"Yes. The car and man she described matched the description of a man that has murdered two people already."

Well, that made him feel good. Leonard suddenly felt even more anxious to see Penny. Rushing toward his room, he remembered his manners, turning again. "Thank you."

Agent Lisbon nodded to him.

* * *

"I swear to God, Jane, what was that about?"

"What was what about?" He cocked his head, trying to look innocent.

"Tell him that she's unconcious, and all beaten up so badly! Why the exaggeration? I warned you about this before we came here..." Lisbon's eyes bore into him. Ooh, she was angry again, Jane thought with delight.

"It was the perfect way to get a reaction out of him. If he knew anything about the incident he would have registered a different kind of surprise then if he was just learning of it, or he would have said something that would prove that he knew I was lying."

"You know I hate it when you-"

"Eliminate a suspect for you right off the bat? Don't lie, you love it when I do that."

"I do not."

"Yes...you do."

"I should just shoot you," she said, shaking her head.

"Well, you could, but I know that...oh, look at this, a Green Lantern statue, now this is facinating." He strolled over and picked it up. The bottom fell off, along with two pieces of paper. "They keep one hundred dollars in the rear end of a Sci-Fi character..."

"He's baffled. Look at that," Van Pelt said.

Lisbon just rolled her eyes.

**That's the beginning. We have the crime, we have the characters...I promise Howard, Raj, Rigsby, Cho, and others will appear in future chapters, as will the whole motive deal...it'll be a bit complicated, but I have it outlined, so I'll update as soon as I can!**


	2. Chapter 2

**Okay, here's chapter two. Sorry this hasn't been updated in a while; I had a deadline for my LJ challenge fic to meet and also I was doing Forensics and that took a lot of my time. Now that the season is over for Forensics and the next deadline isn't for a few months, I can work on updating my neglected fics.**

**I still own nothing.**

"Only a moment, please," said the nurse. "And be very gentle with her."

"Yes. Yes, ma'am. I will, thank you, ma'am." Leonard went inside the room and stopped short.

Penny lay in the hospital bed, beneath the stark white sheets. Her hair was away from her face, which accentuated the blackness around her left eye. Her arms were bruised, from what Leonard could see of them, and her broken finger was in a brace. Taking a shaky breath, Leonard came over to the bed. "Penny?"

She opened her eyes and her bright smile took over her bruised face. "Hey, Leonard."

"What happened? You look horrible."

She glanced down at her arms. "You should see the other guy."

God was he glad that she could joke. "Very funny."

"I'm serious. You should see him. I beat him up and I bet he's not feeling to good about that right now. He's ugly as hell, too."

"Seriously, though. What did he do to you?"

"Beat me. He had some sort of stick. Punched me, too. But I wrestled the stick away from him and bashed his head in." Leonard raised an eyebrow. "Okay, so I didn't bash in his head. I'm pretty sure I broke his arm though."

"Good going," he said holding his hand up. She gave him a high-five with her uninjured hand.

There was then a light knocking at the door. Agent Lisbon stood in the threshold with an Asian cop who's arms were folded. "Hi. Do you feel up to answering a few questions?"

"Um…yeah, sure," Penny said, shifting her weight so she was more upright. "I talked to Agent Rigsby and Agent Cho earlier."

"Yes, she did," said the other cop. "You detailed the attack, and described your attacker and his getaway car. We looked in your vehicle for prints and hair samples, and we made an inventory of everything found there. Could you look this over and see if anything is missing?"

Leonard raised an eyebrow. Agent Cho's voice was monologue, he kept the same expression constantly and didn't change his tone even in separate sentences. Sheldon would twitch like hell if he had to spend any amount of time listening to the guy.

"Yeah," Penny said, taking the clipboard from Agent Cho. "I didn't really have much in that car…nothing worth stealing, anyway." She scanned the list.

"You're going to catch whoever did this, aren't you?"

"We're going to do the best we can, of course," said Agent Lisbon. "He's killed two people already, and we haven't found any connection between the two victims aside from profession, and the profession doesn't relate to you, so if this is the same person we still need to find the connection."

Penny handed the clipboard back. "I don't see anything missing…"

"What was the profession of the two dead people?" Leonard asked.

"Research scientists. They had different specific fields, but both focused on research."

Leonard felt uneasy, realizing something. "Can I see that list of things from her car?"

Agent Cho handed them over. "What's wrong, Leonard?" Penny asked as he scanned the list frantically. Suddenly, Penny sat up. "Your folder!"

"Folder?" Agent Lisbon asked, cocking her head.

"Damn," Leonard said, reaching the end of the list. "Aww, _crap_!"

"A folder is missing?"Cho asked, his arms still folded.

"What folder?" Lisbon asked, making a note on the clipboard after taking it from Leonard. "What does this tell us?"

"The connection isn't with Penny," said Leonard, looking over at her. _This is my fault. _"It's with me."


	3. Chapter 3

**So, so sorry, once again, about not updating! I'd like to say I have a lot going on, but I really don't, just some summer reading. Anyway, here's chapter three; I hope some people still have an interest in this!**

"With you?" Agent Lisbon asked, cocking her head. "How so?"

"The folder contained papers from my trip to Switzerland in February," Leonard said. "Inside were…some pretty important notes on how the Large Hadron Collider works."

"Why would someone want your notes?" Agent Cho asked.

Leonard shrugged, glancing down at Penny again. He knew she was okay, but knowing that _his_ papers were the reason this happened to her made him feel awful. She was looking at the cops, but seemed to feel his gaze. She looked up at him and smiled, her hand sliding over to where his left one rested on the bed. "I really don't know," Leonard said. "They don't let just anybody in to see the collider, it's a very large, very expensive scientific machine."

"And when were you there, exactly?" Cho asked.

"February fourteenth through sixteenth. I flew in on the morning of the fourteenth with a colleague of mine. It was supposed to be her going, but she got sick." Leonard gestured to Penny with a tilt of his head.

Lisbon glanced at Cho, then looked back at Leonard. "Is it…possible," she said hesitantly, "that the colleague might have done this?"

"Raj?" Leonard and Penny said in unison.

"Raj wouldn't lay a hand on her," Leonard said. "Or anyone."

"It wasn't him," Penny said firmly. "I know who Raj is, and he looked nothing like this guy."

"Were the two of you lovers?" Asked a voice.

Leonard, Penny, Lisbon, and Cho's heads turned to the doorway, where Jane stood. "_What?_" Penny said, appalled.

Jane nodded. "Yeah, I didn't think so." He came into the room, holding a muffin in his hand. "Hospital food is normally tasteless, but these are quite good. Want a bite?" He offered the muffin to Lisbon.

She gave him an annoyed smile. "No thanks."

"Want me to get you one?" He pointed in the direction of the hallway. "There's plenty out there."

"Jane? Stop it."

He shrugged, grinning at Leonard and Penny. "Her loss, right?"

"I'm sorry," Leonard said, looking at the agents. "Can we get back to figuring out who stole my particle accelerator files?"

"Agent Van Pelt is speaking with the people who processed your vehicle," Lisbon said to Penny. "My team has the highest clearance rate in the state. We'll find the guy."

Penny smiled thinly. "Okay, thanks." She looked around the room. "How long am I going to have to stay here?"

Lisbon shrugged, shaking her head slowly. "I…really don't…you'll have to talk to the hospital staff about that. Once you're out we'll post an agent at your apartment for protection until we find the person who did this."

"Protection?" Leonard looked at the cops. "You think that the guy might come back?"

"Do you have any other papers relating to the Large Hadron Collider?" Lisbon asked. "Or could someone think that you do?"

"The Large Hadron Collider!" Jane said, face breaking into a grin. "You went to see that? That's fascinating." He looked at Cho. "The scientists there smash-" he made a smashing motion with his fists-"tiny subatomic particles together at super fast speeds so they can burst apart for us to take a little peek at what's inside."

"Is that so?" Cho said in typical monotone.

"Yes," Jane said, looking at Leonard. "_Fas_cinating. Lucky guy." He looked at Lisbon, who was glaring at him. "I think I'm going to get her a muffin," he said in a stage whisper to Cho. "She's very cranky."

"He's gone." Lisbon stated the obvious as Jane exited the room. "Now we can get back on task. Cho," she said, looking at the other cop, "go make sure he doesn't come back in here."

"Yes, boss."

"I have a few files on my laptop," Leonard said, "but nothing really important. Just…general notes, I guess. But I guess that if the person who did this is looking for something that he doesn't find in my folder, he could try and see if I had any more information." He put his hand up to his forehead, feeling harried. "I wish I knew what he was looking for!"

"Well, we will do our best to figure it out," Lisbon said, smiling. She looked at Penny. "We'll let you get some rest now." She headed for the door, motioning for Leonard to follow.

"Can't he stay?" Penny asked, not letting Leonard's hand go even as he stood up. She looked between him and Lisbon. "He's not guilty of anything."

"It's okay with me," Lisbon said, "but once the hospital staff says he has to go, he'll need a ride home. You need some quiet time to get better, and the doctors know best."

Penny tugged on Leonard's hand until he sat back down. "When he leaves," she said to the cop, "I want someone with him. It's his work; I just happened to be there when they went after it."

"I'll get agent Rigsby on that," Lisbon said, smiling at them. She turned and headed down the hall, in the opposite direction from Jane and Cho.

When they were alone, Leonard leaned over to kiss Penny's forehead, then raised her hand to his lips, kissing her on the knuckles, holding her hand in both of his. "I'm so sorry."

She added her other hand to their tangle of fingers. "Don't blame yourself. It's a good thing it was me; I don't think you could have fought back with such Nebraskan force."

He smiled down at her affectionately. "You're probably right." Penny closed her eyes. "Are you tired?" he asked her.

She shook her head. " Leonard?"

"Hmmm?"

"Is the guy going to come after Raj, too?"

Leonard shook his head, then remembered that her eyes were closed. "I doubt it. I was the listed scientist on that trip. He was the guest. I think he'll be okay."

"Good." She brought their hands up to the side of her face and rested her cheek against them. "Don't leave until I fall asleep, okay?"

"I thought you weren't tired."

"I'm not." She opened her eyes and smiled when she saw the look on his face. "Okay, so I am." Her expression became more serious. "But I don't want you leaving the hospital. There's so many people here. Out there…" her voice trailed off, and when it came back, it was quieter, and wavering. "_He's_ out there."

Leonard carefully climbed onto the bed and lay on his side next to her, easing his arm over her stomach and putting his nose next to hers. "How's this?" He asked, smiling

"Perfect."

Penny didn't fall asleep as soon as she would have liked. She was tired, but she was scared, too, and fear always overpowered the need to rest. She wasn't concerned for herself anymore. She was terrified that whoever wanted the information on the supercollider would stop at nothing to get it. And she was terrified that Leonard would somehow get in the way.

* * *

"Okay, everyone," Lisbon said an hour later. "Break is over."

"Aww, Lisbon," Jane said looking up from his book. "I'm just getting to the part where-"

"Don't care," she said, trying to hide her smirk at Jane reading a children's book in the waiting room. "Cho, I need you to take Jane to the comic book store down the street to talk with the owner. He's an ex-boyfriend of the woman down the hall and friend of Dr. Hoftstadter and his colleague. He's friends with a man whom Dr. Cooper says will stop at nothing to humiliate Dr. Hofstadter, Dr. Cooper, and Penny. See if they know anything about what happened." She looked at the other two agents. "Van Pelt, I need you to stay in that hospital room until she's ready to leave, and then go home with her and make sure no one can get to her without your knowing. Rigsby" she said to the dark haired man sitting next to Van Pelt, "Dr. Hofstadter will be going back to the apartment building momentarily. You're sticking with him until we get to the bottom of this.

"Yes boss," Rigsby said, rising and putting his jacket on.

"Everyone go!" Lisbon said, and the agents headed for the door.

Jane tapped Lisbon on the shoulder. "Here." He handed her a muffin. "They are quite good."

"Go with Cho," she said, taking it. "And no hypnotizing!"

"Got it!" Jane waved as he followed Cho out the door.

Lisbon bit into the muffin, chewing slowly. "Not bad," she said to herself.


	4. Chapter 4

**Sorry this hasn't been updated in a while! Blame my school. Actually, blame my school, my sport, and my job for being crazy right now. I've been so busy, but I had some time tonight so I made a slideshow music vid for LP (up on YT tomorrow, hopefully) and wrote this. Hope you like!**

**I still own nothing.**

"This really isn't necessary," Leonard said, reaching behind him to make sure the apartment building's main door didn't close on Agent Rigsby.

"We think it is," he said, taking a bite of his apple. "If whoever hurt your girlfriend is after something of yours, then you're a target that needs to be protected."

"Someone protecting me is someone who isn't helping investigate who hurt Penny," Leonard reasoned, retrieving his mail. "Come on," he added, heading for the stairs. He knew that it was smart to have someone with him, but he couldn't help but think of Penny. At least she was kept in a room surrounded by staff who would keep an eye on her.

"So why isn't the elevator working?" Rigsby asked.

"It…broke. A long time ago. No one ever complained, so we just started using the stairs. Right now it's just an empty shaft."

"Has anyone ever gotten hurt?"

"No, the doors are pretty difficult to open, so an accident is near impossible, and the morale here is pretty high." Leonard had meant to joke on the last part, but it came out too serious. Maybe the situation was too serious to successfully make a joke.

"That's always good," said Rigsby.

Upon reaching 4A, Leonard unlocked the door and went inside. "So…what now?" He asked Rigsby. "Do I just have to stay here?"

"It's recommended that you aren't out and about," Rigsby told him. "People could take shots at you."

_That was pretty blunt. _"Does that happen often?"

"No," he said, shrugging. "I'm just saying…never mind." He shook his head, looking embarrassed.

"So…" Leonard said, sinking down in his chair. "What's the rest of the police doing?"

"They work in shifts. Watching Penny, working on files, interviewing suspects…we're checking out Wil Wheaton and that Stuart guy."

"Wil Wheaton? Stuart?" Leonard was confused. "They didn't do it! Wheaton's out to get Sheldon, not me, and Stuart wouldn't hurt a fly, much less Penny. He has a crush on her."

"Could that be motive?"

Leonard shook his head. "He's not that kind of guy."

"And you're sure that you have no idea who did this?" Rigsby had been standing next to the coffee table, but now he sat on the couch and faced Leonard. "Think."

Leonard folded his hands and looked down at them, considering all of the people he knew. He couldn't think of a single person who would have the motive and the persona to do something like this. "No," he said, shaking his head. "I really can't. Everyone liked her, and…although I don't like admitting this, I'm not working on anything spectacular. No one would want to take my work-they'd take something that had a legitimate chance at being a major discovery."

Rigsby nodded. "I see." His phone buzzed, and he held up a finger to signal to Leonard that he needed a moment. "Sorry. Hello?" He listened for a moment. "Really? Okay…yeah, I'm here. Sounds good. See you in a few." He hung up and looked at Leonard. "Agent Van Pelt is bringing your girlfriend home. We're going to be hanging out in her apartment once she gets here, since it's already been cleared by forensics."

Leonard thought he'd caught on. "And I'm leaving all of my files and notes in this apartment?"

Rigsby nodded. "There'll be two of us here to watch for him if he returns. Can you call your room mate and ask him if he's on his way home?"

Leonard nodded and dialed Sheldon. After explaining the situation, Leonard listened to Sheldon's plan. "I'll go to Howard's house. He'll let me sleep in a bed tonight. But if this gets to dangerous I'm going home to Texas, where the most hazardous matter is a descendant of a chicken that terrorized me when I was a child."

"Sounds good, Sheldon," Leonard said. "He's staying with a friend, and may go visit his family," he told Rigsby.

"Sounds good. Is there anyone else who comes to the apartment regularly?"

"Our two friends, but Sheldon's heading over to one of their place's now, so they won't come over here."

"Okay." Rigsby pulled out his phone again. "Hey boss," he said after a minute. "We're going to have everyone secured within the hour. Uh-huh. Okay, yep." He hung up. "Remember," he said to Leonard, "when they get here, we need to stay in her apartment. If anyone leaves, it could endanger one or more lives. Understood?"

"Understood."

"Leonard!" Penny said happily when she entered her apartment to find him and the other cop sitting on the couch. Her boyfriend got up and wrapped his arms around her. "Hey, Penny," he said, running his hand through her hair.

"I didn't notice anyone following us," Van Pelt said to Rigsby. "So we should be secure in here. We'll just need to close the shades and lock the door."

"We'll be in her room," Leonard said, pulling away from Penny to look at the agents, his arms still around her waist.

"That's fine," Van Pelt said. "But if you hear anything strange out here, stay in there and make sure the door is shut tightly, okay?"

"Okay," Penny said, tugging on Leonard's sleeve. They entered her room and she eased down on the edge of the bed. "How long do you think we'll have to wait?"

"Hard to say," Leonard said. "That team has the highest clearance rate in the state, but that doesn't mean that the man will play right into their hands." He sat down next to her, putting one arm around her shoulders and taking her hand with the other. "What do you want to do?"

"Leonard!" she said, looking appalled. "There's people in the other room!"

He looked at her in confusion for a moment, and then understood. Both of them started laughing. "That's not what I meant, and you know it," he said teasingly. "Do you want to watch a movie? Play Alphabet Movie Characters?"

"Can we play Alphabet Movie Characters while snuggling?" Penny asked, easing herself farther up on the bed.

He smiled affectionately at her. "We sure can." He crawled up next to her and lay down, sliding his arms around her while she put her curled fists against his chest. "Want to start?"

"Margaret Tate."

"Even Piell."

Penny bit the corner of her lower lip, thinking. "Lando Calrissian."

He raised his eyebrows. "Nice."

"Who?"

Leonard realized that the letters matched up. "No, I was commenting on yours." He thought for a moment. "Nute Gunray."

They continued, until finally Leonard couldn't come up with another character that started with an H. "Okay," he said, smiling affectionately at Penny. "You win. Round two? Alphabet Television Characters?" Penny smiled, then froze. "What-" Leonard started, but she put a finger to his lips.

"Shhhh." She motioned with her head toward the living area. "Do you hear anything?"

"No."

"Exactly. They were talking. Now they've stopped."

**I'll try to get chapter five up soon! Meanwhile, review!**


	5. Chapter 5

**Updating quickly! Partly because I have time, and partly because nothing really happened in the last chapter, which was on purpose, but I didn't want to leave you guys waiting with nothing but a little bit of a cliffhanger. (Glad you liked that, Brit!) So here is the next chapter. I have no idea how many more there will be, maybe as few as two. But I'm not sure.**

**DISCLAIMER: I own the suspect guy. But other than that, nothing. Diddly squat. :D**

Leonard let go of Penny's hand and sat up. "_What are you doing?_" She hissed.

"_Relax_," he said in a whisper. "_I'm just going to peek out the door._" He stood and walked toward the door, doing his best to step lightly.

"_Be careful_," she said, getting up.

"_Stay there_!" He said, holding his arm out in an attempt to block her path.

She rolled her eyes and sank down on the end of the bed. Once he was certain that she wasn't going to move, Leonard stepped close to the door and turned the knob quietly. Cracking it open, he peered out into the living area.

Agent Wayne Rigsby was standing near the apartment door, which was open. He held a gun at his side. "_Be careful, Grace," _he whispered. Or, Leonard thought that he said that. This was a time that he wished Sheldon was here with his Vulcan hearing.

"What's he saying?" Penny asked. He turned around with a finger to his lips, and she clapped a hand over her mouth. "_Sorry._"

Leonard turned around and peeked out the door again. Agent Rigsby's gun was held straight out in front of him. Suddenly he bolted forward, disappearing. "Police! Freeze!"

Leonard closed the door and was back on the bed in an instant, curling his arms around Penny. "Someone's out there!" He could feel Penny's nails digging into his back as she clung to him. "_Just don't make a sound_," he whispered. He felt her nod.

A minute went by. Then too. "_Leonard_?" Penny whispered. "Can we hide in the closet?" She motioned with her head toward the door. _"I thought I heard something."_

"_Are you sure? Maybe you're just paranoid. And even if you did, maybe it's the cops_."

"_Wouldn't they call out to us_?" Penny asked.

Leonard looked at her. "_Closet it is._"

Van Pelt followed Rigsby, less than a pace behind. A few feet in front of them was a man, taking the stairs three at a time in his effort to get away. She knew Rigsby could tackle him, but he was waiting for the last set of stairs so they couldn't fall too far. As they reached the final landing, her expectations came true. Rigsby leapt forward, wrapping his arms around the man's shoulders and they went down, skidding down the stairs and ending up on the floor, the man pinned under Rigsby's weight. "Hands behind your back," he yelled, grabbing the man's wrists. "Cuffs!"

Van Pelt pulled her set of handcuffs and knelt beside Rigsby, passing him the cuffs.

"It doesn't matter that you've got me," said the man, craning his neck around to see them. "My partner will find what he needs!"

"Yeah, I bet he will," Rigsby said sarcastically.

Van Pelt put her cell phone to her ear. Lisbon answered on the first ring. "Van Pelt. Any news?"

"We caught a man in the doorway of apartment four A.," she said. "He'd gotten the door open but turned and headed for the stairs-we've cuffed him now."

"Has he said anything?"

"Said something about a partner," Van Pelt said.

"I do have one! You'll never stop both of us!" The man yelled fiercely, spit coming from his mouth.

"Did you hear that?" Van Pelt asked flatly.

"I did. How's the couple?"

"We told them to stay in her bedroom," Van Pelt said. "I'll head up there now to tell them."

"Good. I'll send Cho over to help transport the suspect."

Grace Van Pelt reached the fourth floor landing and quietly opened the apartment door. "It's Agent Van Pelt!" she called ahead of her. Then she froze.

The apartment was messier than she and Wayne had left it. It wasn't ransacked, but clearly someone had been there. Van Pelt withdrew her gun cautiously, backing up when she reached the bedroom door, which was open. She paused, and then jumped forward, landing in the threshold and holding her gun out in front of her. She looked left, and then looked right. No one.

She moved to the bathroom door. It was half open, and when she peered around it, she saw nowhere that anyone could be hiding. The shower curtain was pushed aside, revealing an empty tub.

Van Pelt turned and exited the bathroom, heading for the closet. Holding her gun ready, she used the tip of her boot to pull the door open from the bottom. It was empty.

"Damn." Van Pelt holstered the gun and let out a fierce sigh. "Damn it!" Pulling out her phone, she dialed Lisbon reluctantly. She rarely had it was that she had to make this call; it didn't make doing it any better. "Boss? Bad news."

**Hope you liked it!**


	6. Chapter 6

**Okay, so I'm updating fast because I'm taking advantage of some precious spare time and trying to finish some of my unfinished fics. I will finish "The Equine Expansion" once Kaley returns to work in a week or two, and "The Penny War Antagonism" and "The Marathon Analogy" will be updated as I have time. This one is older so I'm spending more time on it.**

**Still own nothing.**

"How could this have happened?" Agent Lisbon asked. Rigsby and Van Pelt sat in front of her, heads low. Lisbon was borderline furious. Sure, they'd caught twenty year old Darryl Warden, but his bragging about a partner in crime wasn't helping them find the missing couple. Hopefully Jane would get somewhere with Warden so they would have some sort of lead. "What did you guys do?"

"We were in the living room, talking, when Rigsby heard something. I got out my gun and headed for the door. Upon opening it-" Van Pelt paused to take a breath-"I saw 4A's apartment door open. I moved into the hall and saw Warden standing in it. I yelled for him to turn around, and he bolted out the door and down the stairs. Rigsby followed me down them, passed me, and tackled him. He started shouting about a partner. When I went upstairs to let the couple know, they were gone. I searched the apartment; nothing appeared to be missing, and they…weren't in the apartment."

Lisbon gave a frustrated sigh. "Well, somehow you lost them. And now what are we going to do? We have no leads, no blood trails, no fingerprints."

"We do have one clue," said a voice behind her. "We have how the criminal entered the apartment."

Lisbon turned. "Jane. What did you get out of Warden?"

"Oh, I'm lucky I got anything at all. If he wasn't so arrogant, so eager to show off, he never would have said anything. But he's too proud of his job, way too proud…"

"What did he tell you?" Lisbon snapped.

"Easy, easy." Jane put a hand on her shoulder. "Take a few deep breaths."

Lisbon clenched her teeth. "Jane, I swear to God…"

"He was in the apartment as a lookout. Whoever was working with him was already there. Warden was there as a decoy-he wanted you two to see him and chase him, leaving his accomplice a few more moments to search without the fear of being noticed."

"How did you two miss this?" Lisbon asked incredulously, looking at Rigsby and Van Pelt. They glanced at each other and then looked down, unable to meet their boss's eyes. "You were kissing!" She accused, her nose twitching in anger. "I told you guys…" she trailed off, unable to speak. "Are you aware of what your little affair is doing to this case? I'm going to report this if the case doesn't end well! And by well, I mean _perfectly_!"

"You weren't aware that this started up again?" Jane asked. "It's been a month."

"Shut up, Jane!"

"So you don't want to know how the partner got into the other apartment?" Jane asked. Lisbon glared at him, but he continued anyway. "He crawled out of the window in Dr. Hofstadter's bedroom and crawled around the building into the bedroom window of Miss Penny."

"Oh, come on, that's not possible."

"It's very possible," said a voice. Lisbon turned. Cho and a tall, pale, skinny man stood a few paces behind them. Dr. Hofstadter's roommate. "When I was traumatized by a break-in that occurred last year, I crawled from my bedroom to Leonard's on the sill. The aforementioned sill continues around the building. As I am not blessed with athletic skills, it would be very possible for someone who is to crawl from one window to the other."

Cho looked at Lisbon. "He showed up near the end of our interview with the comic book store owner and Wheaton. Both of them are cleared."

"So…" Lisbon said, trying to make sense of everything, "he didn't find what he was looking for…"

"Or he found it and was looking elseware to make sure he didn't miss anything," Rigsby interjected.

"…and he crawled around into the other apartment to make sure he wasn't missing anything else. There he found our missing couple, and took them? How would he get them out of the building? He didn't take them down the stairs, the elevator isn't working, and he couldn't have gotten them out of the window and down the side of the building. Unless you've done that, too," she said, looking at Sheldon, who shook his head.

"We found no signs of a struggle in the bedroom," Van Pelt said quietly.

Lisbon sighed. "Well, let's go and find something to go off of with what he have. It's our only option." She looked at Cho. "Have you cleared the apartment building?"

"Yes. All residents are staying in hotels on the outskirts of L.A."

"Good." Lisbon turned back to the sullen agents sitting before her. "You two," she said. "Go back to 4A and rip that place apart." At this, the roommate started. "Relax," she said to him. "They're going to do a thorough scrutiny with _no_ distractions and see if they can find any clues to what the motive could be."

"It's been two days and you've failed to establish motive?" Sheldon said in surprise. "And why wasn't the apartment gone over thoroughly earlier today, when my friends were kidnapped?"

"We've been putting our energies into looking for them," Lisbon explained. "We sealed off the building so it would be ready when we came to look it over. That time is now." Glaring at Rigsby and Van Pelt, she motioned with her head to the door. "Go. Redeem yourselves." She pointed at Sheldon. "Take him with you."

"_Penny? It's been hours. I'm sure he's gone."_

"_But how do we get out of here?" _ She whispered back. Leonard slid his arms around her waist. "_We have to wait for someone to show up."_

"_I'm sure they'll be back soon. They'll be looking for us."_

She shivered. It was cold down here. Cold and dark and dirty. But they were safe at least. _"This was a good idea," _she whispered. _"How did you think of it?"_

He smiled in the dark, his hands finding hers and grabbing them, attempting to keep them warm. Odd how much colder it was in here. _"I dreamed it once. Years ago."_

He could feel her head turn against his shoulder. "You dreamed about going down the elevator shaft via cables?" she said in a normal voice.

He smiled again. "Yeah…I have odd dreams sometimes."

"I didn't think we'd be strong enough to hang on."

"Well," Leonard said, shifting his weight slightly. "If we were doing something totally crazy like you hanging on to me, we'd probably end up falling. But the two of us going one by one…well, it's only thirty feet, so I knew our upper body strength would hold out."

"You're so smart," she said affectionately.

Leonard thanked his subconscious. Penny snuggled up closer to him. "It was so scary when we heard that man coming around the windowsill."

"Yeah, but it would have been worse if he'd come in through the door. Then we'd have been forced _out_ the window and onto the sill. At least this way, we were able to leave the apartment door and head down here."

"Yeah." Penny sighed. "I just want to get out of here."

"Me too," he said, pushing his chin into the crook of her neck. "Me, too."

**There you go, Brit! I figured I had to tell you where they were. The next chapter will probably be the last. Hopefully, it'll be up within the week. But I can't make any promises.**

**I'd love reviews! Real, well-rounded reviews would be awesome. I appreciate every single one I get, but when I put a lot of effort into a chapter and I get reviews like ":D" or "awesome update" I feel like they're obligatory. Tell me what you liked or didn't like! That's what a review is for!**

**Ending my rant now. :D**


	7. Chapter 7

**Okay, here's the last chapter. I really enjoyed writing this, though it was hard. And I have only seen one Season Three episode of The Mentalist, so I had to go back and watch a few season one episodes on my DVD to get a feel for the characters again. Hope this doesn't disappoint!**

**I own the characters I've created. That's it.**

"You have to find them!" Sheldon stated again as the two cops and himself entered the apartment he shared with Leonard.

"We're working on it," said Agent Van Pelt, attempting to calm the strange man. "We're trying."

"No, no, that's not good enough! There _is_ no try, you either succeed or fail. And as of right now, you're failing."

"We're working on it," said Agent Rigsby. "Our team has the highest clearance rate in the state; we're doing all that we can."

"Cleary, you're doing a poor job. If it wasn't for two apparent professionals falling victim to their primitive biological urges, Leonard and Penny never would have gone missing. I'm putting full blame on the two of you."

Van Pelt sighed. Yes, it was their fault, and it wasn't the first time they'd let their on and off relationship affect a case they were working on. She knew it was unprofessional, too. It really did suck when your personal life and work overlapped.

"Grace!"

She jumped out of her thoughts, looking over at Rigsby, who raised an eyebrow at her. "Sorry, what?"

"Give me a hand with this couch?"

Van Pelt circled the couch and lifted the end, herself and Rigsby scooting it backwards a foot or so. "Nothing under here," she said.

"Is that really necessary?" Sheldon asked. "Moving all of the furniture around?" He stood next to the end of it, frowning.

"We'll put everything back," Rigsby assured him.

The look on Sheldon's face was one of horror. "What else have you…oh, God." He ran toward the bedrooms.

"This is probably the strangest case we've ever worked on," Van Pelt said, glancing down at her feet. "Eureka!"

"What?" Rigsby asked as she bent and picked something off of the ground. "What is it?"

"A cross," she said, holding it up. "I have this same one."

"Is it yours?" he asked.

"No," Van Pelt said, reaching inside her vest and withdrawing a cross identical to the first. "Here's mine. This is another one."

"Could it belong to Dr. Hofstadter or Dr. Cooper?"

Van Pelt shook her head. "They're studying string theory and dark matter and…other stuff; I don't think that, even if they are religious, they'd have these things lying around. Diests, at most."

"Hmmm. You think the killer left it here, then?"

"Wayne," Van Pelt said slowly. "Could this be motive?"

"What do you…?" Rigsby cocked his head.

Van Pelt held a hand up as she pulled her phone out of her pocket with the other one, dialing and holding the phone up to her ear.

"Van Pelt. What do you have?"

"We found a cross in Dr. Hofstadter's apartment."

"And it doesn't belong to them?"

"Unlikely." Van Pelt held up the cross in questioning as Sheldon re-entered the room. _Yours?_ She mouthed. Sheldon looked at it and shook his head. _Not anyone's here,_ he mouthed back, exaggerating his words. "No, confirmed negative. I was thinking that the killer might be angry about the work done in Geneva. Some of the tests done there could, to some extent, be considered 'playing God'."

"Then why wouldn't they go around killing people who are working in cloning?" Lisbon asked.

"Well, Boss," Van Pelt said after a moment's thought. "There's a lot of different careers that threaten Christianity; it just depends how strongly you feel about it."

"Boss," said Rigsby, taking the phone from Van Pelt. "If they feel like finding those particles in the collider would disprove Creation, then wouldn't the work being done in Europe be the _most_ threatening to Christianity?"

"It's possible," said Lisbon. "Keep looking; I'll get Cho and Jane to work on Warden a little more, see if we can get more out of him. Good job."

"Thanks, Boss," said Rigsby, hanging up and handing the phone back to Van Pelt.

"Dr. Cooper," said Van Pelt, putting the cross into an evidence bag, "has Dr. Hofstadter or yourself ever received angry phone calls or letters regarding your work?"

Silence. "Dr. Cooper?" Van Pelt questioned, sealing the bag and turning around when he still didn't answer. She found him standing next to the couch, frozen, eyes darting about. "May I ask what you're...?"

"_Shhhhh_!" He hissed, putting a finger to his lips. Van Pelt stopped talking, raising a finger to her own lips to silence Rigsby when he entered the room a moment later. After a few more moments, Sheldon darted out into the hall.

* * *

"_It's really dark in here._"

"Yeah, it is," Leonard agreed. They couldn't see a thing. "And you don't have to whisper, Penny."

"Oh, right." She let out a giggle. "I've just gotten used to it."

"How's your arm?" he asked.

He couldn't see her roll her eyes in the dark, but he knew that she did. "It's fine, Leonard. Just as fine as it was ten minutes ago. And ten minutes before that."

"You're making those numbers up," he accused. "You have no way of knowing how long it's been."

Suddenly, a sound came from one of the walls that made up the elevator shaft. A tap. Then another. Then another. Then a voice. "Leonard and Penny?" _Tap, tap tap. _"Leonard and Penny?" _Tap tap tap._ "Leonard and Penny?"

"Sheldon!" Penny screeched, jumping up. She slipped and fell back onto Leonard, who had been trying to rise. He fell backward and she landed on top of him. "Sorry," she said as they scrambled up. "Sheldon!" she shouted, knocking back on the wall. "We're in here!"

"I know that!" came his indignant voice. "I wouldn't have summoned you from here if I didn't know that's where you were. I could hear your annoying jibber jabber from the apartment."

"Don't you just love his Vulcan hearing?" Leonard said to Penny, wrapping his arms around her waist again.

"Are you guys okay?" came another voice-a female voice.

"Agent Van Pelt!" Penny said. "Can you get us out?"

"We'll head down to the first floor," called Van Pelt.

Leonard and Penny waited, Penny shaking in relief, as they listened to the sounds of people running down the stairs. When the sounds stopped, Leonard called out. "Are you here?"

"Hang on," came a male voice. "Van Pelt, give me a hand with this."

Leonard and Penny heard sounds of things being dragged, metal on metal, and then, suddenly, their dark space was flooded in light. They were in the lobby, well, sort of. The first floor stopped at their waists, they were actually standing on a surface a few feet below that. Just above them, on the first floor, stood Van Pelt, Rigsby, and "Sheldon!" Penny shrieked, putting her hands on the floor and vaulting herself up. "Ow," she said, almost as an afterthought as she rubbed her arm. Standing up, she threw her arms around the theoretical physicist.

Behind her, Leonard crawled out of the shaft and entered the group hug. Penny and Sheldon each adjusted an arm to go around him. "I was worried about you guys," Sheldon admitted.

"Aw, that's sweet," Penny said. She stepped back. "Have you figured out who it is yet?"

"We may have a new lead," Van Pelt said. "We're checking it out right now."

"Good," Penny said.

"Come down to the station and we'll catch you all up," Rigsby offered. "We'll be heading there in a few minutes."

At that moment, Leonard and Sheldon realized that they were still hugging. They jumped back, startled.

* * *

Policeman Gerald Cranmer took a drink of his coffee, frowning at the coolness of the liquid. Ever since his insulated mug had broken – unbreakable, his ass – his coffee never stayed warm the entire morning. The only way to drink all of it when it was warm was to guzzle, and then he'd have to pee part way through his shift. He glanced down at his Patrick McManus book, a favorite from his days of growing up in the states. Well, his boss was the Sneed of Geneva police; he'd know for sure if Cranmer took a bathroom break when he was supposed to be driving around.

He was contemplating pouring the rest out of the window of his squad car when his radio crackled to life. "_All available personnel, report to the Large Hadron Collider!"_

* * *

"Thank you," said Agent Lisbon, nodding even though the person on the other end of the line couldn't see her. She glanced up at where Penny, Leonard, and Sheldon sat and nodded to them. "Uh huh. Yes, we'll keep in touch. Thank you. Okay. Bye." She hung up, rose from her seat, and walked over to where the trio sat. "Okay," she began. "This morning, well, very recently, morning in Geneva, a man was caught trying to bomb the Large Hadron Collider."

"What?" Leonard and Sheldon said in unison.

"A man by the name of Gerald Cranmer made the arrest, and upon interrogation, the man revealed that he was working for a man by the name of Ethan Sommers, who had instructed him to destroy the 'God Defying Device'."

"Ethan Sommers," Leonard said, shaking his head. "Never heard of him."

"He's a religious extremist who was born and raised in Massachusettes. That's all we know about him. His last known location was in Great Falls, Montana, two months ago. Apparantly the man caught in Geneva was bribed and then threatened by Sommers to attempt to damage the Collider. Sommers doesn't want any scientific experiments of that type being performed."

"Will you find him?" Leonard asked, his arm around Penny.

"We will. He can't stay hidden forever."

* * *

Patrick Jane lay on his couch, staring up at the stain on the ceiling. Today, it looked like the Flash…or maybe the superhero obsession of the people of the recent case was causing him to fall victim to power of suggestion. That was a weakness he'd have to overcome.

"Excuse me?" Came a voice. Jane tipped his head, seeing a rather short, skinny man standing in front of him. "Hello, sir."

"Hello," Jane said. "Do I know you?"

The man shook his head. "No, you don't. I…I was at the airport this morning, coming in from Helena, and I saw this lying on a table." He held up a laptop. "It says 'L.H.' on the top, and I thought it might be the laptop that was listed in the paper last time I visited here. The one stolen from that _physicist_. It said…said something a-about a reward…?"

Jane looked at the man curiously. "Um…yes. Yes, just wait right here." He motioned to the couch. "Sit."

Jane made himself walk slowly down the hall where he knew Lisbon was. "_Lisbon_," he hissed.

"Yeah?" she asked him.

"Sommers is here."

"What?" Lisbon looked confused. "Where?"

"My couch."

"How do you know?" she asked.

"Simple," Jane said. "I put an add in the paper, for a laptop with the initials L.H. on the top, that was missing, and I'd give $2500 for the return of it. Figured that would be enough to flush him out, since his original motive was shot to hell." He glanced over his shoulder. "And he said he flew in from Helena. Helena is in Montana, just like his last known location. Think about it, Lisbon! He's a nervous man, just the type to get someone else to bomb the Collider for him. And now that his accomplices are in custody, he figures he can come and get a little money off the return of the laptop, as there was nothing useful on it."

"Well, maybe he did find it."

"The L.H. initials are very small," Jane said. "No one would notice that in passing. And it's been six days since the attempted bombing; he may feel more comfortable coming now."

"I'm on it," Lisbon said, convinced. She slipped her gun out of its holster and marched back down the hall. "Ethan Sommers! FBI!"

* * *

"Thank you so much," Penny said once more as the agents left the apartment later that day. "So much."

"No problem," said Lisbon. "We're just glad you're all okay."

Penny impulsively hugged Agent Van Pelt, pulling back and smiling at the rest of them. "We really appreciate everything you've done."

"It was all me, really," Jane started, and Lisbon swatted his arm. The group laughed.

When they had gone, Penny turned and smiled at Leonard, Sheldon, Howard, and Raj. "It's over," she said happily. "All three are arrested."

"They still have trial," Leonard reminded her. "We'll have to see them again."

"I don't care," said Penny, kissing him. "We'll bust them; no way they don't get thrown in prison for a long time!"

Sheldon shuddered. "I hope they don't mind urinating in public."

**Hope you enjoyed it! Sorry if the ending felt a little rushed.**


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